Don't forbid unknown files in a library

The current code forbids any files it does not know about, but this is
bad because:
 - It breaks forward compatibility if we later add more files or
   directories to the library format.
 - It breaks for people who want to have some extra stuff in their
   library (say, .gitignore or a README file). We can't keep a list of
   "allowed" stuff, since there will always be stuff missing.

This commit removes that code and just allows all files again.
Reintroduced warning on development leftovers in 1.5 libraries.

See #1692
Updated msys-1.0.dll to the latest version for Windows 8.1 compatibility.

Removed windows/avr_tools.zip, the binary distribution is now downloaded
from the Arduino repository.

Fixes #1658
Revert "EEPROM library to the new format"

This reverts commits:
3223d4fdca32ec03de4a3a2a0c22f2d40de5f374
77f8dd63ab102ab5d2929ac4edd5c00ae9d70493
Revert "SPI library to new format"
Detect version of bridge.py running on the Yun.
Update version to 1.5.5 (Base.java)
Added missing File::size() method to Bridge.
Fixed typo
Implemented multi-byte read in File::read of Bridge library.